How to programmatically register an addon
To answer the specific question, I think you're looking for this: https://www.blender.org/api/blender_python_api_2_57_release/bpy.ops.wm.html#bpy.ops.wm.addon_enable

For example:

import bpy
bpy.ops.wm.addon_install(filepath='/home/my-addons/awesome.py')
bpy.ops.wm.addon_enable(module='awesome')


Regarding the part of your posting where you say "when I ship my entire Blender folder to another developer" .. I suggest you make your solution turn-key and provide an install script that points blender to your .py file and registers needed addons. Maybe something along the lines of:

#!/usr/bin/env bash
blender --background --python /path/to/addon-installer.py
echo "Done"